8QGF | pdb_00008qgf

CRYSTAL STRUCTURE OF AS-ISOLATED M148L MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII

PDB DOI: https://doi.org/10.2210/pdb8QGF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ralstonia pickettii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-09-05 Released: 2024-09-11
Deposition Author(s): Petchyam, N., Antonyuk, S., Hasnain, S.S.
Funding Organization(s): UK Research and Innovation (UKRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free:
0.162 (Depositor), 0.161 (DCC)
R-Value Work:
0.134 (Depositor), 0.132 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structural studies of haem three-domain copper nitrite reductase mutants from Ralstonia pickettii

Petchyam, N., Antonyuk, S., Hasnain, S.S.

To be published.

Macromolecule Content

Total Structure Weight: 49.34 kDa
Atom Count: 4,553
Modeled Residue Count: 454
Deposited Residue Count: 454
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A	454	Ralstonia pickettii	Mutation(s): 1 EC: 1.7.2.1
UniProt
Find proteins for I6NAW4 (Ralstonia pickettii) Explore I6NAW4 Go to UniProtKB: I6NAW4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I6NAW4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.162 (Depositor), 0.161 (DCC)
R-Value Work: 0.134 (Depositor), 0.132 (DCC)
R-Value Observed: 0.135 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.952	α = 90
b = 127.952	β = 90
c = 86.249	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	BB/N013972/1
UK Research and Innovation (UKRI)	United Kingdom	BB/L006960/1

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.